LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp  275.0 275.0 100.0 tchain 1

shell "rm -f out*.colvars.*"
fix		2 all colvars peptide.colvars
fix		2a ref setforce 0.0 0.0 0.0

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles

#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars:  https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "one"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "two"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new "harmonic" instance.
colvars:   # name = "h_pot"
colvars:   # colvars = { one, two }
colvars:   # outputEnergy = off [default]
colvars:   # timeStepFactor = 1 [default]
colvars:   # writeTISamples = off [default]
colvars:   # writeTIPMF = off [default]
colvars:   # centers = { 10, 10 }
colvars:   # targetCenters = { 10, 10 } [default]
colvars:   # outputCenters = off [default]
colvars:   # forceConstant = 100
colvars:   # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    292.14604 
      10    305.06149   -5058.8972   -6286.1901    1227.2929   -6413.1021      58.8499    103.38345 
      20    311.00516   -4999.0612    -6250.266    1251.2048   -6417.1021    47.695297    36.699695 
      30    314.22337   -4993.7012   -6257.8532     1264.152   -6421.9679    35.344144    10.563933 
      40    297.87491   -5020.8378   -6219.2184    1198.3805   -6389.8528    27.723133    3.8354517 
      50    304.02071   -5056.2576   -6279.3633    1223.1057   -6456.8214    55.459505   0.20678217 
      60    285.92576   -5104.0461    -6254.354    1150.3079   -6435.5814    32.767229   0.69352945 
      70    277.83519   -5163.9758   -6281.7345    1117.7587   -6447.7033    39.627168    11.433603 
      80    267.51495   -5206.4046    -6282.644    1076.2394   -6456.6369    31.611883    6.3554178 
      90    278.15579   -5245.3824    -6364.431    1119.0485   -6499.8063    28.849773   0.36941576 
SHAKE stats (type/ave/delta) on step 100
  4 1.11098 8.97155e-05
  6 0.996996 1.00568e-05
  8 1.08 6.02345e-06
  10 1.111 1.84253e-05
  12 1.08 7.2713e-06
  14 0.959996 0
  18 0.957198 3.36079e-05
  31 104.52 0.0030599
     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms

Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.5817     | 1.5817     | 1.5817     |   0.0 | 72.79
Bond    | 0.0031469  | 0.0031469  | 0.0031469  |   0.0 |  0.14
Kspace  | 0.17366    | 0.17366    | 0.17366    |   0.0 |  7.99
Neigh   | 0.37354    | 0.37354    | 0.37354    |   0.0 | 17.19
Comm    | 0.013652   | 0.013652   | 0.013652   |   0.0 |  0.63
Output  | 0.00026059 | 0.00026059 | 0.00026059 |   0.0 |  0.01
Modify  | 0.025484   | 0.025484   | 0.025484   |   0.0 |  1.17
Other   |            | 0.001615   |            |       |  0.07

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11124 ave 11124 max 11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708237 ave 708237 max 708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2

run     100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 100
  4 1.11098 8.97155e-05
  6 0.996996 1.00568e-05
  8 1.08 6.02345e-06
  10 1.111 1.84253e-05
  12 1.08 7.2713e-06
  14 0.959996 0
  18 0.957198 3.36079e-05
  31 104.52 0.0030599
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
     110    266.26438   -5341.1991   -6412.4073    1071.2082   -6552.7551    33.573173    1.9229657 
     120    262.66604   -5386.2387   -6442.9704    1056.7317   -6587.5483    29.859587    2.7124812 
     130    252.83379   -5422.5401   -6439.7157    1017.1756   -6580.4703    25.979343    1.2031592 
     140    253.85111   -5452.1838   -6473.4522    1021.2684   -6609.4826    26.071651   0.30585517 
     150    261.31816   -5490.4727   -6541.7817    1051.3091   -6646.6076    16.258823    6.9051008 
     160     255.7352   -5521.5941   -6550.4424    1028.8483   -6658.1373    19.717399    12.339679 
     170    253.42527   -5540.0942   -6559.6494    1019.5552   -6656.6678    23.293812    10.290217 
     180    248.51161   -5550.3253   -6550.1124    999.78705   -6661.4235    26.200127    3.4336038 
     190    250.80862   -5555.2554   -6564.2836    1009.0282    -6666.164     25.53634    3.3494288 
SHAKE stats (type/ave/delta) on step 200
  4 1.111 1.81266e-06
  6 0.997 7.79424e-07
  8 1.08 1.08903e-06
  10 1.111 2.96503e-07
  12 1.08 4.69038e-07
  14 0.960001 0
  18 0.957201 3.76471e-06
  31 104.52 0.000411055
     200    251.50475   -5557.4251   -6569.2538    1011.8287   -6674.0845    24.804906    7.1387574 
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms

Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.5975     | 1.5975     | 1.5975     |   0.0 | 78.58
Bond    | 0.0033164  | 0.0033164  | 0.0033164  |   0.0 |  0.16
Kspace  | 0.17349    | 0.17349    | 0.17349    |   0.0 |  8.53
Neigh   | 0.21971    | 0.21971    | 0.21971    |   0.0 | 10.81
Comm    | 0.012045   | 0.012045   | 0.012045   |   0.0 |  0.59
Output  | 0.00026226 | 0.00026226 | 0.00026226 |   0.0 |  0.01
Modify  | 0.025034   | 0.025034   | 0.025034   |   0.0 |  1.23
Other   |            | 0.001596   |            |       |  0.08

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11159 ave 11159 max 11159 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708083 ave 708083 max 708083 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708083
Ave neighs/atom = 353.335
Ave special neighs/atom = 2.34032
Neighbor list builds = 7
Dangerous builds = 0

fix 2 all colvars peptide.colvars input out.colvars.state output out2
colvars: Resetting the Collective Variables module.

run     100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars:  https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "one"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new collective variable.
colvars:   # name = "two"
colvars:   Initializing a new "distance" component.
colvars:     # name = "" [default]
colvars:     # componentCoeff = 1 [default]
colvars:     # componentExp = 1 [default]
colvars:     # period = 0 [default]
colvars:     # wrapAround = 0 [default]
colvars:     # forceNoPBC = off [default]
colvars:     # scalable = on [default]
colvars:       Initializing atom group "group1".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars:       Initializing atom group "group2".
colvars:       # name = "" [default]
colvars:       # centerReference = off [default]
colvars:       # rotateReference = off [default]
colvars:       # atomsOfGroup = "" [default]
colvars:       # indexGroup = "" [default]
colvars:       # psfSegID =  [default]
colvars:       # atomsFile = "" [default]
colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars:       # enableForces = on [default]
colvars:       # enableFitGradients = on [default]
colvars:       # printAtomIDs = off [default]
colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars:     # oneSiteSystemForce = off [default]
colvars:     # oneSiteTotalForce = off [default]
colvars:   All components initialized.
colvars:   # timeStepFactor = 1 [default]
colvars:   # width = 1 [default]
colvars:   # lowerBoundary = 0 [default]
colvars:   # upperBoundary = 0 [default]
colvars:   # expandBoundaries = off [default]
colvars:   # extendedLagrangian = off [default]
colvars:   # outputValue = on [default]
colvars:   # outputVelocity = off [default]
colvars:   # outputTotalForce = off [default]
colvars:   # outputAppliedForce = off [default]
colvars:   # subtractAppliedForce = off [default]
colvars:   # runAve = off [default]
colvars:   # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars:   Initializing a new "harmonic" instance.
colvars:   # name = "h_pot"
colvars:   # colvars = { one, two }
colvars:   # outputEnergy = off [default]
colvars:   # timeStepFactor = 1 [default]
colvars:   # writeTISamples = off [default]
colvars:   # writeTIPMF = off [default]
colvars:   # centers = { 10, 10 }
colvars:   # targetCenters = { 10, 10 } [default]
colvars:   # outputCenters = off [default]
colvars:   # forceConstant = 100
colvars:   # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars:   Restarting collective variable "one" from value: 10.0128
colvars:   Restarting collective variable "two" from value: 9.62236
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: Setting initial step number from LAMMPS: 200
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 200
  4 1.111 1.81266e-06
  6 0.997 7.79424e-07
  8 1.08 1.08903e-06
  10 1.111 2.96503e-07
  12 1.08 4.69038e-07
  14 0.960001 0
  18 0.957201 3.76471e-06
  31 104.52 0.000411055
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
     200    251.50475   -5557.4251   -6569.2538    1011.8287   -6674.0845    24.804906    7.1387574 
     210    253.15303   -5538.5615   -6557.0215      1018.46   -6672.0498     37.67662   0.61219496 
     220    245.19621    -5522.519   -6508.9679    986.44888   -6628.1899    36.657688   0.04864338 
     230    258.69884   -5495.7275   -6536.4988    1040.7713   -6658.2885    34.857911   0.22092547 
     240    260.79635   -5469.8678   -6519.0776    1049.2098   -6624.1801    31.576951    3.7574816 
     250    269.07527   -5438.3946   -6520.9114    1082.5167   -6616.4383    25.447674    8.6600014 
     260    266.01049   -5397.3485   -6467.5353    1070.1868   -6580.2897    26.871917    8.3323097 
     270    272.81313    -5350.882   -6448.4365    1097.5545   -6563.8231    23.114195    10.973131 
     280    279.42263   -5307.9798    -6432.125    1124.1452   -6557.3367    33.644027    8.5490492 
     290    286.85172    -5260.841   -6414.8741    1154.0331   -6515.6798    28.574838    5.9100133 
SHAKE stats (type/ave/delta) on step 300
  4 1.111 1.79792e-05
  6 0.997005 1.02512e-05
  8 1.08 1.85102e-05
  10 1.111 9.98839e-06
  12 1.08 8.84111e-06
  14 0.960008 0
  18 0.957203 1.8445e-05
  31 104.52 0.00168383
     300    291.52798    -5216.288   -6389.1341    1172.8462   -6503.1276    27.889154    2.2482459 
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms

Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.6047     | 1.6047     | 1.6047     |   0.0 | 77.46
Bond    | 0.0031033  | 0.0031033  | 0.0031033  |   0.0 |  0.15
Kspace  | 0.17325    | 0.17325    | 0.17325    |   0.0 |  8.36
Neigh   | 0.25117    | 0.25117    | 0.25117    |   0.0 | 12.12
Comm    | 0.012173   | 0.012173   | 0.012173   |   0.0 |  0.59
Output  | 0.00026488 | 0.00026488 | 0.00026488 |   0.0 |  0.01
Modify  | 0.025317   | 0.025317   | 0.025317   |   0.0 |  1.22
Other   |            | 0.001731   |            |       |  0.08

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11296 ave 11296 max 11296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708152 ave 708152 max 708152 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708152
Ave neighs/atom = 353.369
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0

colvars: Resetting the Collective Variables module.

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:06
